diff --git a/main/main.cpp b/main/main.cpp
index 22a31d597e6..e6fba3c7b47 100644
--- a/main/main.cpp
+++ b/main/main.cpp
@@ -2090,6 +2090,11 @@ void Main::cleanup() {
 
 	ERR_FAIL_COND(!_start_success);
 
+	if (script_debugger) {
+		// Flush any remaining messages
+		script_debugger->idle_poll();
+	}
+
 	ResourceLoader::remove_custom_loaders();
 	ResourceSaver::remove_custom_savers();